| addDataProcessing_(ConsensusMap &map, const DataProcessing &dp) const | TOPPBase | protected |
| addDataProcessing_(FeatureMap &map, const DataProcessing &dp) const | TOPPBase | protected |
| addDataProcessing_(PeakMap &map, const DataProcessing &dp) const | TOPPBase | inlineprotected |
| addEmptyLine_() | TOPPBase | protected |
| CANNOT_WRITE_OUTPUT_FILE enum value | TOPPBase | |
| checkIfIniParametersAreApplicable_(const Param &ini_params) | TOPPBase | protected |
| checkParam_(const Param ¶m, const String &filename, const String &location) const | TOPPBase | protected |
| debug_level_ | TOPPBase | protected |
| EXECUTION_OK enum value | TOPPBase | |
| ExitCodes enum name | TOPPBase | |
| EXTERNAL_PROGRAM_ERROR enum value | TOPPBase | |
| findEntry_(const String &name) const | TOPPBase | protected |
| getDocumentIDTagger_() const | TOPPBase | protected |
| getDoubleList_(const String &name) const | TOPPBase | protected |
| getDoubleOption_(const String &name) const | TOPPBase | protected |
| getFlag_(const String &name) const | TOPPBase | protected |
| getIniLocation_() const | TOPPBase | inlineprotected |
| getIntList_(const String &name) const | TOPPBase | protected |
| getIntOption_(const String &name) const | TOPPBase | protected |
| getParam_() const | TOPPBase | protected |
| getParamArgument_(const Param::ParamEntry &entry) const | TOPPBase | protected |
| getProcessingInfo_(DataProcessing::ProcessingAction action) const | TOPPBase | protected |
| getProcessingInfo_(const std::set< DataProcessing::ProcessingAction > &actions) const | TOPPBase | protected |
| getStringList_(const String &name) const | TOPPBase | protected |
| getStringOption_(const String &name) const | TOPPBase | protected |
| ILLEGAL_PARAMETERS enum value | TOPPBase | |
| INCOMPATIBLE_INPUT_DATA enum value | TOPPBase | |
| INPUT_FILE_CORRUPT enum value | TOPPBase | |
| INPUT_FILE_EMPTY enum value | TOPPBase | |
| INPUT_FILE_NOT_FOUND enum value | TOPPBase | |
| INPUT_FILE_NOT_READABLE enum value | TOPPBase | |
| inputFileReadable_(const String &filename, const String ¶m_name) const | TOPPBase | protected |
| INTERNAL_ERROR enum value | TOPPBase | |
| log_type_ | TOPPBase | protected |
| main(int argc, const char **argv) | TOPPBase | |
| main_(int, const char **) | TOPPOpenPepXL | inlineprotectedvirtual |
| makeTempDirectory_() const | TOPPBase | protected |
| MISSING_PARAMETERS enum value | TOPPBase | |
| official_ | TOPPBase | protected |
| outputFileWritable_(const String &filename, const String ¶m_name) const | TOPPBase | protected |
| paramEntryToParameterInformation_(const Param::ParamEntry &entry, const String &argument="", const String &full_name="") const | TOPPBase | protected |
| paramToParameterInformation_(const Param ¶m) const | TOPPBase | protected |
| PARSE_ERROR enum value | TOPPBase | |
| parseRange_(const String &text, double &low, double &high) const | TOPPBase | protected |
| parseRange_(const String &text, Int &low, Int &high) const | TOPPBase | protected |
| preprocessPairs_(const PeakMap &spectra, const vector< pair< Size, Size > > &spectrum_pairs, const double cross_link_mass_iso_shift, double fragment_mass_tolerance, double fragment_mass_tolerance_xlinks, bool fragment_mass_tolerance_unit_ppm) | TOPPOpenPepXL | inlineprotected |
| printUsage_() | TOPPBase | protected |
| registerDoubleList_(const String &name, const String &argument, DoubleList default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerDoubleOption_(const String &name, const String &argument, double default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerFlag_(const String &name, const String &description, bool advanced=false) | TOPPBase | protected |
| registerFullParam_(const Param ¶m) | TOPPBase | protected |
| registerInputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList()) | TOPPBase | protected |
| registerInputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false, const StringList &tags=StringList()) | TOPPBase | protected |
| registerIntList_(const String &name, const String &argument, IntList default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerIntOption_(const String &name, const String &argument, Int default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerOptionsAndFlags_() | TOPPOpenPepXL | inlineprotectedvirtual |
| registerOutputFile_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerOutputFileList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerParamSubsectionsAsTOPPSubsections_(const Param ¶m) | TOPPBase | protected |
| registerStringList_(const String &name, const String &argument, StringList default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerStringOption_(const String &name, const String &argument, const String &default_value, const String &description, bool required=true, bool advanced=false) | TOPPBase | protected |
| registerSubsection_(const String &name, const String &description) | TOPPBase | protected |
| registerTOPPSubsection_(const String &name, const String &description) | TOPPBase | protected |
| removeTempDirectory_(const String &dirname, Int keep_debug=2) const | TOPPBase | protected |
| setMaxFloat_(const String &name, double max) | TOPPBase | protected |
| setMaxInt_(const String &name, Int max) | TOPPBase | protected |
| setMaxNumberOfThreads(int num_threads) | TOPPBase | static |
| setMinFloat_(const String &name, double min) | TOPPBase | protected |
| setMinInt_(const String &name, Int min) | TOPPBase | protected |
| setValidFormats_(const String &name, const std::vector< String > &formats, const bool force_OpenMS_format=true) | TOPPBase | protected |
| setValidStrings_(const String &name, const std::vector< String > &strings) | TOPPBase | protected |
| setValidStrings_(const String &name, const std::string vstrings[], int count) | TOPPBase | protected |
| test_mode_ | TOPPBase | protected |
| toolName_() const | TOPPBase | protected |
| topp_ini_file_ | TOPPBase | protectedstatic |
| TOPPBase(const String &name, const String &description, bool official=true, bool id_tag_support=false, bool require_args=true, const String &version="") | TOPPBase | |
| TOPPOpenPepXL() | TOPPOpenPepXL | inline |
| UNEXPECTED_RESULT enum value | TOPPBase | |
| UNKNOWN_ERROR enum value | TOPPBase | |
| verboseVersion_ | TOPPBase | protected |
| version_ | TOPPBase | protected |
| writeCTD_() | TOPPBase | protected |
| writeDebug_(const String &text, UInt min_level) const | TOPPBase | protected |
| writeDebug_(const String &text, const Param ¶m, UInt min_level) const | TOPPBase | protected |
| writeLog_(const String &text) const | TOPPBase | protected |
| writeWSDL_(const String &filename) | TOPPBase | protected |
| ~TOPPBase() | TOPPBase | virtual |